BIO403: Biotechnology « Saylor.org – Free Online Courses Built by Professors

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Readings

1.1 Reading: PBS: Lexi Krock's “Anatomy of Photo 51”

Link: PBS: Lexi Krock's “Anatomy of Photo 51” (HTML)

Instructions: Please investigate the critical evidence that led to the model of the DNA double helix. Rosalind Franklin’s X-ray diffraction image #51 is shown here. Click on the “Launch interactive” button and advance step by step from image #51 to the double helix model of DNA. Please note that all structural parameters of the double helix are provided by image #51.

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1.3 Reading: Access Excellence: Pamela Peters' “What Is Biotechnology?”

Link: Access Excellence: Pamela Peters' “What Is Biotechnology?” (HTML)

Instructions: Please read this page carefully. When you finish it, please continue your reading: Open the “Where Did Biotechnology Begin?” link at the bottom of the page. Please note that making bread, cheese, beer, or wine are all historical biotechnology applications.

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1.3 Reading: BioBasics’ “Full Article: Traditional vs. Modern Biotechnology”

Link: BioBasics’ “Full Article: Traditional vs. Modern Biotechnology” (HTML)

Instructions: Please read this page, focusing on the differences between traditional and modern biotechnology application. Please note that modern biotechnology is able to genetically engineer living organisms, and it often does so.

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2.1 Reading: Nature Education's Scitable: Clare O’Connor’s “Fluorescence In Situ Hybridization”

Link: Nature Education's Scitable: Clare O’Connor’s “Fluorescence In Situ Hybridization” (HTML)

Instructions: Please study the “In Situ Hybridization Is Used to Localize DNA Sequences on Chromosomes,” “Fluorescent Probes Are Introduced,” and “Using FISH to Identify the Positions of Genes” sections on this page. Author Clare O’Connor works in the Department of Biology at Boston College.

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2.2.1 Reading: Dr. Kary Banks Mullis’s “Polymerase Chain Reaction”

Link: Dr. Kary Banks Mullis’s “Polymerase Chain Reaction” (HTML)

Instructions: Please read about Dr. Kary Bank Mullis. It is rare that technological inventions receive a Nobel Prize, but Mullis was awarded the Nobel Prize in Chemistry in 1993 for his invention of the polymerase chain reaction (PCR) method. Please study the main column and click on the “Questions About PCR” (PDF) link on the right and study that section as well.

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2.2.1 Reading: University of South Carolina's School of Medicine: Margaret Hunt’s “Real Time PCR”

Link: University of South Carolina's School of Medicine: Margaret Hunt’s “Real Time PCR” (HTML)

Instructions: Please study this page carefully. You can learn about an advanced PCR application, which is essential in tissue specific gene expression applications. Please note that the first step is to reverse translate RNA to DNA, because we can amplify only DNA in the test tube. Because of the reverse transcriptase step, this method is also called RT-PCR. Here, it gets little confusing since the method is in real time as well, because it follows the PCR product production in real time. The best way to keep all of these aspects in mind is to remember this method as “real time RT-PCR.” Please make sure that you click on the thumbprints to enlarge all the images embedded in the left maroon-colored panel of this site.

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2.2.2 Reading: Evrogen’s “Suppression Subtractive Hybridization (SSH)”

Link: Evrogen’s “Suppression Subtractive Hybridization (SSH)” (HTML)

Instructions: Please learn the content of this page. Please note that subtractive hybridization is a technique that compares the differences between two nucleic acid pools and exponentially amplifies the differences in these pools by PCR. The nucleic acid pools are commonly mRNA pools, thus such experiments generate subtraction cDNA libraries.

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2.3 Reading: Wiley Online Library: Markus Fuhrmann, et al.’s “A Synthetic Gene Coding For the Green Fluorescent Protein (GFP) Is a Versatile Reporter in Chlamydomonas reinhardtii”

Link: Wiley Online Library: Markus Fuhrmann, et al.’s “A Synthetic Gene Coding For the Green Fluorescent Protein (GFP) Is a Versatile Reporter in Chlamydomonas reinhardtii” (HTML or PDF)

Instructions: You may read this as HTML or a PDF. To access the PDF, go to “Article Tools” on the right side of the page and click on “Get PDF.” This is a peer-reviewed publication. Please study the last paragraph of the “Introduction,” the entire “Synthesis of a C. Reinhardtii-Adapted GFP” in the “Results” section, and the entire “Discussion” section on this page. The aim of this project is to exchange the codons in the jellyfish GFP gene to codons that are more frequent in a unicellular alga. Please note that the codon preference varies in different organisms.

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2.4.1 Reading: Nature Education’s Scitable: Suzanne Clancy’s “RNA Functions”

Link: Nature Education’s Scitable: Suzanne Clancy’s “RNA Functions” (HTML)

Instructions: Please study this summary on the regulatory RNAs. Here you will learn that besides the familiar mRNA, tRNA, and rRNA, other RNA functions are abundant in the cell. The following sections will introduce you to several RNA techniques that are designed to modulate gene expression in the cell.

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2.4.2 Reading: Macalester College: Mary Montgomery’s “RNAi”

Link: Macalester College: Mary Montgomery’s “RNAi” (HTML)

Instructions: Please study this page. Please note that RNA interference is an experimental technique.

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2.4.3 Reading: John W. Kimball’s Biology Pages: “Ribozymes”

Link: John W. Kimball’s Biology Pages: “Ribozymes” (HTML)

Instructions: Please study this page.

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2.4.4 Reading: National Center for Biotechnology Information’s PubMed: American Society for Clinical Investigation: Nassim Usman and Lawrence M. Blatt’s “Nuclease-Resistant Synthetic Ribozymes: Developing a New Class of Therapeutics”

Link: National Center for Biotechnology Information’s PubMed:American Society for Clinical Investigation: Nassim Usman and Lawrence M. Blatt’s “Nuclease-Resistant Synthetic Ribozymes: Developing a New Class of Therapeutics” (HTML or PDF)

Instructions: Please study this publication on making synthesized ribozymes. This material is also available in PDF form from the top right corner of the page.

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2.4.5 Reading: National Center for Biotechnology Information’s PubMed: Journal ACS Chemical Biology: Shana Topp and Justin P. Gallivan’s “Emerging Applications of Riboswitches in Chemical Biology”

Link: National Center for Biotechnology Information’s PubMed: Journal ACS Chemical Biology: Shana Topp and Justin P. Gallivan’s “Emerging Applications of Riboswitches in Chemical Biology” (HTML or PDF)

Instructions: Please study this page carefully. This publication is challenging, but it helps you appreciate the regulatory roles of RNA in the cell. Please rely heavily on the illustrations. It is not essential to memorize the names of the metabolites. This material can also be viewed in PDF form from the top right corner of the page. The authors work at Emory University. This is a peer-reviewed publication.

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3.1.1 Reading: Nature Education’s Scitable: Ingrid Lobo and Kenna Shaw’s “Thomas Hunt Morgan, Genetic Recombination, and Gene Mapping”

Link: Nature Education’s Scitable: Ingrid Lobo and Kenna Shaw’s “Thomas Hunt Morgan, Genetic Recombination, and Gene Mapping” (HTML)

Instructions: Please recall crossing over events during meiosis while you are studying this publication. Crossing over causes genetic recombination, and it contributes to offspring diversity. Crossing over events can be utilized to construct genetic linkage maps. Genetic linkage maps place genes at a certain distance on a chromosome. The placement of the genes is relative to each other; their absolute distance stays unknown.

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3.1.2 Reading: John W. Kimball’s Biology Pages: “ Genetic Linkage and Genetic Maps”

Link: John W. Kimball’s Biology Pages: “Genetic Linkage and Genetic Maps” (HTML)

Instructions: Please study the “Genetic versus Physical Maps” section on the page. Please note that physical maps provide the absolute distance of the genes on the chromosome. In situ hybridization of genes on a chromosome is a technique that results in a physical map. The best physical maps derive from genome sequencing projects.

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3.2.1 Reading: National Center for Biotechnology Information’s “Restriction Fragment Length Polymorphism (RFLP)”

Link: National Center for Biotechnology Information’s “Restriction Fragment Length Polymorphism (RFLP)” (HTML)

Instructions: Please study this page. Restriction fragment length polymorphism has been instrumental in mapping genes and in medical diagnosis. RFLP was the first DNA technique employed in forensic laboratories for the identification of individuals.

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3.2.2 Reading: National Center for Biotechnology Information’s “SNPs: Variations on a Theme”

Link: National Center for Biotechnology Information’s “SNPs: Variations on a Theme” (HTML)

Instructions: Please study this page. Single nucleotide polymorphism results from point mutations in a certain position of the DNA sequence. Point mutations may or may not have biological consequences, depending on whether they change the function of the gene product. SNPs have been used in medical diagnosis. A combination of SNPs can be used for identifying individuals and species.

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3.2.3 Reading: Nature Education’s Scitable: P. Z. Myers’ “Tandem Repeats and Morphological Variation”

Link: Nature Education’s Scitable: P. Z. Myers’ “Tandem Repeats and Morphological Variation” (HTML)

Instructions: Please study this page to learn about how repeat number variations can identify individuals in a population. Robust change in the number of repeats in certain genetic positions is also linked to phenotypic changes. Author Dr. Myers works at the University of Minnesota.

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3.2.4 Reading: Davidson College’s: Department of Biology’s “Microsatellite DNA Methodology”

Link: Davidson College’s: Department of Biology’s “Microsatellite DNA Methodology” (HTML)

Instructions: Please study this page. Note that microsatellite polymorphism is similar to VNTRs, but the size of the repeats is shorter. Many applications refer to it as short tandem repeats (STRs).

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3.3.1 Reading: National Human Genome Research Institute’s “Sequence-Tagged Sites, Another Marker”

Link: National Human Genome Research Institute’s “Sequence-Tagged Sites, Another Marker” (HTML)

Instructions: Please study this page. Please note that sequence tagged sites are fundamental in recent genome project techniques. STS sequences have no particular biological significance. STS is a term used when we refer to a method.

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3.3.2 Reading: National Center for Biotechnology Information’s “ESTs: Gene Discovery Made Easier”

Link: National Center for Biotechnology Information’s “ESTs: Gene Discovery Made Easier” (HTML)

Instructions: Please study this page. ESTs serve us well in genome projects and gene expression studies.

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3.3.3 Reading: JGI Genome Portal’s “What Is a Scaffold?”

Link: JGI Genome Portal’s “What Is a Scaffold?” (HTML)

Instructions: Please study this page. Please note that a contig is a set of aligned, overlapping, nucleic acid sequences.

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3.3.4 Reading: Biology Reference’s: Christine Klein’s “Radiation Hybrid Mapping”

Link: Biology Reference’s: Christine Klein’s “Radiation Hybrid Mapping” (HTML)

Instructions: Please study this page. Please note the similarities to mapping with genetic recombination (BIO403 Subunit 3.1.1 Genetic Maps). Radiation mapping is used to determine the relative distance between chromosomal markers.

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3.3.5 Reading: Blackwell Publishing Ltd: Animal Genetics: G. P. Di Meo et al.’s “An Advanced Sheep (Ovis aries, 2n = 54) Cytogenetic Map and Assignment of 88 New Autosomal Loci by Fluorescence In Situ Hybridization and R-Banding”

Link: Blackwell Publishing Ltd:Animal Genetics: G. P. Di Meo et al.’s “An Advanced Sheep (Ovis aries, 2n = 54) Cytogenetic Map and Assignment of 88 New Autosomal Loci by Fluorescence In Situ Hybridization and R-Banding” (HTML or PDF)

Instructions: Please study the “Introduction” section on this page. Cytogenetic mapping generates a physical map of genes on a chromosome. You can access the PDF form from the top right corner of the page.

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3.4.1 Reading: Davidson College’s: Department of Biology’s “Chromosomal Walking to Clone the Cystic Fibrosis Gene”

Link: Davidson College’s: Department of Biology’s “Chromosomal Walking to Clone the Cystic Fibrosis Gene” (HTML)

Instructions: Please study this page. Chromosomal walking can be used to determine the position of a gene in the genome. It is employed only if the genome of the species is not sequenced.

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3.4.2 Reading: Genome News Network: Bijal P. Trivedi’s “Sequencing the Genome”

Link: Genome News Network: Bijal P. Trivedi’s “Sequencing the Genome” (HTML)

Instructions: Please study this page.

Terms of Use: Please respect the copyright and terms of use displayed on the webpage above. The shotgun genome sequencing method has been designed by Craig Venter. This method skips physical mapping.

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3.4.3 Reading: Nature Education’s Scitable: “Chromosomes”

Link: Nature Education’s Scitable: “Chromosomes” (HTML)

Instructions: Please study the “Why Is Complex Packing Critical for Eukaryotic Chromosomes?” section on this page. Please note that heterochromatins are tightly packed regions of the genome at the centromer and telomer regions.

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3.4.3 Reading: National Human Genome Project Institute’s “Drosophila Heterochromatin Genome Project”

Link: National Human Genome Project Institute’s “Drosophila Heterochromatin Genome Project” (HTML)

Instructions: Please read the “Background” section on this page.

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3.4.4 Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “About the Human Genome Project”

Link: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “About the Human Genome Project” (HTML)

Instructions: Please study this page.

Terms of Use: Please respect the copyright and terms of use displayed on the webpage above. Human genome sequencing has been greatly speeded up by the shotgun sequencing method. The sequencing of genomic regions that are rich in repetitive sequences, such as telomeres and centromeres, are still in progress.

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3.4.5 Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “How Many Genes are in the Human Genome?”

Link: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “How Many Genes are in the Human Genome?” (HTML)

Instructions: Please study this page. Please note that we have only estimations on the number of genes in the human genome. These predictions are aided by bioinformatics but should be verified in the future by experiments.

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3.4.6 Reading: Yale University’s Gerstein Lab: “Pseudogene.org: Genome Analysis”

Link: Yale University’s Gerstein Lab: “Pseudogene.org Genome Analysis” (HTML)

Instructions: Please study this page. Follow the link in "What causes pseudogenes to arise?" box for a graphical illustration. Please note that pseudogenes do not have a known biological function.

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3.4.7 Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Lodish, et al.’s Molecular Cell Biology, 4th edition: “Chromosomal Organization of Genes and Noncoding DNA”

Link: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Lodish, et al.’s Molecular Cell Biology, 4^th edition: “Chromosomal Organization of Genes and Noncoding DNA” (HTML)

Instructions: Please study the “Genomes of Higher Eukaryotes Contain Much Nonfunctional DNA” section on this page. Please note that some DNA regions are genes coding proteins or functional RNA products, while other regions are noncoding. Some of the noncoding regions, for example, repeat sequences and pseudogenes and have no known function. These seemingly useless regions are referred as “junk DNA.”

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3.5.1 Reading: National Human Genome Research Institute’s “DNA Microarray Technology”

Link: National Human Genome Research Institute’s “DNA Microarray Technology” (HTML)

Instructions: Please study this page. Please note that microarray is an efficient and widely used high throughput technology of differential gene expression studies.

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3.5.2 Reading: Nature Education’s Scitable: “Scientists Can Study an Organism’s Entire Genome with Microarray Analysis”

Link: Nature Education’s Scitable: “Scientists Can Study an Organism’s Entire Genome with Microarray Analysis” (HTML)

Instructions: Please study this page and watch the video.

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3.5.3 Reading: Brandeis University’s: Jim Haber’s “Chromatin Immunoprecipitation”

Link: Brandeis University’s: Jim Haber’s “Chromatin Immunoprecipitation” (HTML)

Instructions: Please study this page, and follow the “protocol” link on the bottom of the page. Chromatin immunoprecipitation is used to identify interacting proteins and DNA segments.

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3.6.1 Reading: Bio Databases: Houle, et al.’s “Database Mining in the Human Genome Initiative”

Link: Bio Databases: Houle, et al.’s “Database Mining in the Human Genome Initiative” (HTML)

Instructions: Please learn the content of the white paper, from the “Abstract” to the “Conclusion.”

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3.6.2 Reading: PLoS Biology: Ross C. Hardison’s “Comparative Genomics”

Link: PLoSBiology: Ross C. Hardison's “Comparative Genomics” (HTML or PDF)

Instructions: Please study this publication. You can access the PDF format from the top right corner of the page. Genome sequence comparisons can be used to predict gene function between species and between the individuals of a species. It is also used to determine phylogenetic distances among species.

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3.6.2 Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “Functional and Comparative Genomics Fact Sheet”

Link: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “Functional and Comparative Genomics Fact Sheet” (HTML)

Instructions: Please study this page.

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3.7.1 Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “Gene Testing”

Link: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “Gene Testing” (HTML)

Instructions: Please study this page. Gene testing is performed primarily in medical diagnosis. It is also a mostly historical forensic technique for the identification of individuals.

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3.7.1 Reading: National Health Museum’s “Understanding Gene Testing—What Does a Predictive Gene Test Tell You?”

Link: National Health Museum’s “Understanding Gene Testing—What Does a Predictive Gene Test Tell You?” (HTML)

Instructions: Please study this page. Please note that gene testing can link the presence of a gene to the probability of developing a condition (disease) in an individual or in the offspring of an individual.

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3.7.1 Reading: Nature Education’s Scitable: Leslie A. Pray’s “Questionable Prognostic Value of Genetic Testing”

Link: Nature Education’s Scitable: Leslie A. Pray’s “Questionable Prognostic Value of Genetic Testing” (HTML)

Instructions: Please study this page. There is an increasing interest on the environmental factors on trait penetrance. Research should unravel how to take advantage of a genetic prognosis. Environmental factors such as nutrition and personal habits, seem to influence gene expression and the penetrance of traits. Medications can also be developed to decrease the risk of undesired traits (disease).

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3.7.2 Reading: The Royal Society’s “What Is Pharmacogenetics?”

Link: The Royal Society’s “What Is Pharmacogenetics?” (HTML)

Instructions: Please study this page. Please note that individual genetic makeup will influence the response to a medication.

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3.7.2 Reading: Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “Pharmacogenomics”

Link: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “Pharmacogenomics” (HTML)

Instructions: Please study this page. Pharmacogenomics is a way drugs can be designed in the future. It requires knowing individuals' genetic makeup besides the risk factors what doctors use today. It holds the promise of safer and more efficient medication.

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3.8.1 Reading: National Center for Biotechnology Information’s “Systematics and Molecular Phylogenetics”

Link: National Center for Biotechnology Information’s “Systematics and Molecular Phylogenetics” (HTML)

Instructions: Please study this page. Molecular phylogenetics establishes relationship between species based on their genetic material. Before the availability of molecular techniques, species were classified based on their phenotype and behavior.

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3.8.2 Reading: Sandwalk: Larry A. Moran’s “The Evolution of Gene Families”

Link: Sandwalk: Larry A. Moran’s “The Evolution of Gene Families” (HTML)

Instructions: Please study this page by Dr. Moran, Professor of Biochemistry at the University of Toronto.

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3.9.1 Reading: Nature Education’s Scitable: “Systems Biology Allows Us to Think Broadly”

Link: Nature Education’s Scitable: “Systems Biology Allows Us to Think Broadly” (HTML)

Instructions: Please study the diagram. You may want to return to this diagram, as you are completing the remaining subunits in Unit 3.

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3.9.1 Reading: Nature Education’s Scitable: Jill U. Adams’ “Transcriptome: Connecting the Genome to Gene Function”

Link: Nature Education’s Scitable: Jill U. Adams’ “Transcriptome: Connecting the Genome to Gene Function” (HTML)

Instructions: Please study this page by freelancer science writer Dr. Adams in its entirety. Please recall that the genetic material is identical in all somatic cells of a multicellular organism, but a different set of genes is expressed in different cells. The transcriptome is the collection of the expressed genes, and it is different in different cell types.

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3.9.2 Reading: Nature Education’s Scitable: Jill Adams’ “The Proteome: Discovering the Structure and Function of Proteins”

Link: Nature Education’s Scitable: Jill Adams’ “The Proteome: Discovering the Structure and Function of Proteins” (HTML)

Instructions: Please study this page by freelancer science writer Dr. Adams in its entirety. The proteome is the collection of proteins that are expressed. Please note that the proteomes of different cell types are different. Both proteome and transcriptome reflect gene activity.

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3.9.3 Reading: BioTechnique: Ute Roessner and Jairus Bowne’s “What Is Metabolomics All About?”

Link: BioTechnique: Ute Roessner and Jairus Bowne’s “What Is Metabolomics All About?” (HTML or PDF)

Instructions: Please study all three pages of this publication. You can switch to the next page by clicking a number on the bottom of the page. To access the PDF format, click the Full Text (PDF) button on the linked page.

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3.9.3 Reading: Genome Alberta and Genome Canada’s “The Human Metabolome Project”

Link: Genome Alberta and Genome Canada’s “The Human Metabolome Project” (HTML)

Instructions: Please study this page. Please note that the metabolome consists of a variety of unrelated small molecular mass substances. We usually know that these substances are present if they are above the detection limit of an employed analytical technique.

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3.9.4 Reading: Nature Education’s Scitable: Lorenz and Eck’s “Metagenomics and Industrial Applications”

Link: Nature Education’s Scitable: Lorenz and Eck’s “Metagenomics and Industrial Applications” (PDF)

Instructions: Please study this publication carefully. Metagenome is the genetic information, which is extracted from an environmental microbial population. It contains genetic material from multiple living organisms.

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3.9.4 Reading: Nature Education’s Scitable: Kira Zhaurova’s “Genomes of Other Organisms: DNA Barcoding and Metagenomics”

Link: Nature Education’s Scitable: Kira Zhaurova’s “Genomes of Other Organisms: DNA Barcoding and Metagenomics” (HTML)

Instructions: Please study this page. Please compare the nature of full genome sequences and metagenomic data.

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4.1.1 Reading: Davidson College: Department of Biology’s “SDS-PAGE (PolyAcrylamide Gel Electrophoresis)”

Links: Davidson College: Department of Biology’s “SDS-PAGE (PolyAcrylamide Gel Electrophoresis)” (HTML)

Instructions: Please study this page. Please note that electrophoresis can be used to separate substances, which have electrical charge. In the SDS-PAGE technique, proteins are associated with SDS, thus they become negatively charged. Furthermore, the smaller SDS-associated proteins will travel faster in the electric field than the larger ones.

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4.1.2 Reading: Davidson College: Department of Biology’s “Western Blot Procedure”

Links: Davidson College: Department of Biology’s “Western Blot Procedure” (HTML)

Instructions: Please study the outline of the Western blot analysis. This procedure is also called immunoblot technique, because it is utilizing antibodies to detect specific proteins in a mixture. In reality, antibodies are not absolutely specific, thus this method may produce a false positive or negative signal.

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4.2.1 Reading: Jim Clark’s ChemGuide: “High-Performance Liquid Chromatography—HPLC”

Link: Jim Clark’s ChemGuide: “High-Performance Liquid Chromatography—HPLC” (HTML)

Instructions: Please study this page. Please note that HPLC is used to purify peptides; it is not a typical protein purification method.

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4.2.2 Reading: John W. Kimball's Biology Pages: “Affinity Chromatography”

Link: John W. Kimball's Biology Pages: “Affinity Chromatography” (HTML)

Instructions: Please study this page. Please note that affinity chromatography is a very efficient purification technique as long as the immobilized molecule binds strongly and specifically to the protein of interest. Antibody-antigen interaction is an example of strong and specific binding.

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4.2.2 Reading: Davidson College: Department of Biology’s “Affinity Chromatography Method”

Link: Davidson College: Department of Biology’s “Affinity Chromatography Method” (HTML)

Instructions: Please study the outline of the Affinity Chromatography Method.

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4.2.3 Reading: Florida State University: Michael Blaber’s “Protein Purification: Column Chromatography—Ion Exchange; Dialysis and Concentration”

Link: Florida State University: Michael Blaber’s “Protein Purification: Column Chromatography—Ion Exchange; Dialysis and Concentration” (HTML)

Instructions: Please study this page. Please note that proteins are typically purified from a biological sample. Ion exchange chromatography is a low efficiency, but inexpensive purification technique. It is oftentimes employed to remove substances from a complex mixture, which would otherwise interfere with the following specific purification step.

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4.3.1 Reading: Wikibooks’ “Protein Primary Structure”

Link: Wikibooks’ “Protein Primary Structure” (PDF)

Instructions: Please learn the “Edman Degradation” section on this page.

Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0 (HTML). You can find the original Wikibooks version of this article here (HTML).

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4.3.2 Reading: The University of Leeds: Alison Ashcroft’s “An Introduction to Mass Spectrometry”

Link: The University of Leeds: Alison Ashcroft’s “An Introduction to Mass Spectrometry” (HTML)

Instructions: Please study sections “1. What Is Mass Spectrometry (MS)? What Information Does Mass Spectrometry Provide?” and the content of subsections “4.1 Introduction,” “8.1 Tandem Mass Spectrometry,” “8.2 Tandem Mass Spectrometry Analyses,” and “8.3 Peptide Sequencing by Tandem Mass Spectrometry “ on this page.

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4.4.1 Reading: John W. Kimball’s Biology Pages: “Proteomics”

Link: John W. Kimball’s Biology Pages: “Proteomics” (HTML)

Instructions: Please study “The Yeast Two-Hybrid System” section on this page.

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4.4.2 Reading: National Center for Biotechnology Information’s Bookshelf: Garland Science: Alberts, et al.’s Molecular Biology of the Cell, 4th edition: “Analyzing Protein Structure and Function”

Link: National Center for Biotechnology Information’s Bookshelf: Garland Science: Alberts, et al.’s Molecular Biology of the Cell, 4^th edition: “Analyzing Protein Structure and Function” (HTML)

Instructions: Please study "Affinity Chromatography and Immunoprecipitation Allow Identification of Associated Proteins" section on this page.

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4.4.3 Reading: Functional Genomics: Mike Taussig and Oda Stoevesandt’s “Protein Arrays Resource Page”

Link: Functional Genomics: Mike Taussig and Oda Stoevesandt’s “Protein Arrays Resource Page” (HTML)

Instructions: Please study this page. Please note that there are different types of protein arrays. Protein arrays represent a more recent development of high throughput screening compared to DNA microarrays.

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4.5.1 Reading: European Molecular Biology Laboratory’s “Protein Expression and Purification Core Facility: Protein Expression E. coli”

Link: European Molecular Biology Laboratory’s "Protein Expression and Purification Core Facility: Protein Expression E. coli” (HTML)

Instructions: Please study this page. Please note that E. coli can be employed to express a functional protein only if the biological function of the protein does not require posttranslational modification.

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4.5.2 Reading: John W. Kimball’s Biology Pages: “Gene Regulation in Eukaryotes”

Link: John W. Kimball’s Biology Pages: “Gene Regulation in Eukaryotes” (HTML)

Instruction: Please study this page. Focus on the differences between eukaryotic and prokaryotic genes expression, including posttranslational modifications.

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4.5.2 Reading: BioPharm International: Rudolph et al.’s “Expression of Recombinant Proteins in Yeast”

Links: BioPharm International: Rudolph et al.’s “Expression of Recombinant Proteins in Yeast” (HTML)

Instructions: Please study this page. Please note that Pichia pastoris and other yeast hosts have the capability to modify recombinant proteins posttranslationally. Posttranslational modification is an essential feature of biologically active proteins.

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4.5.3 Reading: BioMed Central: BMC Biotechnology: Nehlsen et al.’s “Recombinant Protein Expression by Targeting Pre-Selected Chromosomal Loci”

Link: BioMed Central: BMC Biotechnology: Nehlsen et al.’s “Recombinant Protein Expression by Targeting Pre-Selected Chromosomal Loci” (HTML or PDF)

Instructions: Please read the “Background” section found under “Abstract” on this page. You can access the PDF version from the righthand side of the page, under "viewing options." This is a peer-reviewed publication.

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4.5.4 Reading: National Center for Biotechnology Information's Bookshelf: Lodish, Berk, Zipursky, et al.’s Molecular Cell Biology, 4th edition: “Protein Glycosylation in the ER and in Golgi Complex”

Link: National Center for Biotechnology Information's Bookshelf: Lodish, Berk, Zipursky, et al.’s Molecular Cell Biology, 4^th edition: “Protein Glycosylation in the ER and in Golgi Complex” (HTML)

Instructions: Please study this entire section from Lodish, Berk, Zipurksy, et al.’s Molecular Cell Biology textbook. Please note that protein glycosylation is very important for certain proteins to function properly in eukaryotes. Proteins that are expressed in prokaryotic cell, for example, in E. coli, cannot be glycosylated, because these cells lack membrane-bound subcellular organelles.

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4.6.1 Reading: Scientific Electronic Library Online Brazil: Brazilian Journal of Medical and Biological Research: J.M. Yon’s “Protein Folding: A Perspective for Biology, Medicine and Biotechnology”

Link: Scientific Electronic Library Online Brazil: Brazilian Journal of Medical and Biological Research: J.M. Yon’s “Protein Folding: A Perspective for Biology, Medicine and Biotechnology” (HTML or PDF)

Instructions: Please study the content of “Protein Folding in Biotechnology: Protein Engineering and Design” on this page. You can access the PDF version from the right hand side of the page. Author Yon works at the Institut de Biochimie, Biophysique Moléculaire et Cellulaire, UMR CNRS, Université de Paris-Sud, Orsay, France.

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4.6.2 Reading: Oxford University Press’s Journal of Experimental Biology: Jeanneau, et al.’s “Manipulating PEPC Levels in Plants”

Links: Oxford University Press’s Journal of Experimental Biology: Jeanneau, et al.’s “Manipulating PEPC Levels in Plants” (HTML or PDF)

Instructions: Please study this article. Review what you have learned about RiBisCo, and focus on the “Transgenic Plants” section on this page. You can access the PDF version by clicking the “Full Text (PDF)” button on the right-hand side of the page. This is a peer-reviewed publication.

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4.6.3 Reading: Oxford University Press’s Nucleic Acids Research: Sleight et al.’s “In-Fusion BioBrick Assembly and Re-Engineering”

Links: Oxford University Press’s Nucleic Acids Research: Sleight et al.’s “In-Fusion BioBrick Assembly and Re-Engineering” (HTML or PDF)

Instructions: Please study this entire article. Focus on the “Introduction,” “Results,” and “Discussion” sections. You can access the PDF from the right-hand side of the page. This is a peer-reviewed publication. The authors work at the Department of Bioengineering, University of Washington, Seattle.

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4.6.4 Reading: The FASEB Journal: Budisa, et al.’s “Toward the Experimental Codon Reassignment In Vivo: Protein Building With an Expanded Amino Acid Repertoire”

Link: The FASEB Journal: Budisa, et al.’s “Toward the Experimental Codon Reassignment In Vivo: Protein Building With an Expanded Amino Acid Repertoire” (HTML or PDF)

Instructions: Please focus on the " 'Restricted' vs. 'Relaxed' Genetic Code" and "Codon Reassignment In Living Cell" sections. You can access the PDF from the right-hand side of the page. The authors work at the Max Planck Institut für Biochemie, Germany. This is a peer-reviewed publication.

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4.6.5 Reading: BioMed Central: BMC Medicine: David Davis and David Stokoe’s “Zinc Finger Nucleases as Tools To Understand and Treat Human Diseases”

Link: BioMed Central: BMC Medicine: David Davis and David Stokoe’s “Zinc Finger Nucleases as Tools To Understand and Treat Human Diseases” (HTML or PDF)

Instructions: Please focus on the following sections: “Methods for Design, Testing and Implementation of Zinc Finger Proteins (ZFPs):” “Addition of Functional Domains Expands the Utility of ZFPs:” and “Addition of Eendonuclease Activities to ZFPs to Create Targeted DNA Scissors.” Please note that domain recombination is the recombining of two known functional domains of proteins to create a new kind of protein. You can access the PDF from the right-hand side of the page. Authors work in the Department of Molecular Biology at Genentech Inc. This is a peer-reviewed publication.

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4.6.6 Reading: National Center for Biotechnology Information’s Bookshelf: Wiley-Liss: Strachan and Read’s Human Molecular Genetics, 2nd edition: “Chapter 14: Our Place in the Tree of Life”

Link: National Center for Biotechnology Information’s Bookshelf: Wiley-Liss: Strachan and Read’s Human Molecular Genetics, 2^nd edition: “Chapter 14: Our Place in the Tree of Life” (HTML)

Instructions: Please study the “14.5.2 Exon Shuffling Permits Diverse Combinations of Structure and Functional Modules, and May be Mediated by Transposable Elements” section on this page.

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4.6.7 Reading: National Center for Biotechnology Information’s PubMed: PLoS Biology: David R. Halpin and Pehr B. Harbury’s “DNA Display II. Genetic Manipulation of Combinatorial Chemistry Libraries for Small-Molecule Evolution”

Link: National Center for Biotechnology Information’s PubMed: PLoS Biology: David R. Halpin and Pehr B. Harbury’s “DNA Display II. Genetic Manipulation of Combinatorial Chemistry Libraries for Small-Molecule Evolution” (HTML or PDF)

Instructions: Please study “Strategy” in the “Results” section. You can access the PDF from the top right corner of the page. The two authors, Halpin and Harbury, work in the Department of Biochemistry at Stanford University’s School of Medicine. This is a peer-reviewed publication.

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4.6.8 Reading: National Center for Biotechnology Information’s Bookshelf: Harvard Stem Cell Institute: Stephanie M. Willerth and Shelly E. Sakiyama-Elbert’s StemBook: “Combining Stem Cells and Biomaterial Scaffolds for Constructing Tissues and Cell Delivery”

Link: National Center for Biotechnology Information’s Bookshelf: Harvard Stem Cell Institute: Stephanie M. Willerth and Shelly E. Sakiyama-Elbert’s StemBook: “Combining Stem Cells and Biomaterial Scaffolds for Constructing Tissues and Cell Delivery” (HTML or PDF)

Instructions: Please study this page. You can access the PDF from the right-hand side of the page under the “Download” section. The two authors, Willerth and Sakiyama-Elbert, are affiliated with the Department of Biomedical Engineering at Washington University, St. Louis.

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5.1.1 Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates: S.F. Gilbert’s Developmental Biology, 6th edition: “Pollination”

Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates: S.F. Gilbert’s Developmental Biology, 6^th edition: “Pollination” (HTML)

Instructions: Please study this excerpt from Giblert’s textbook in its entirety.

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5.1.2 Reading: University of Notre Dame: Lauren Willoughby’s “Selective Breeding and Hybridization”

Link: University of Notre Dame: Lauren Willoughby’s “Selective Breeding and Hybridization” (HTML)

Instructions: Please study this page. Please note that humans have modified living organisms historically.

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5.1.3 Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Miller, Suzuki, et al.’s Introduction to Genetic Analysis, 7th edition: “Mutation Breeding”

Link: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Miller, Suzuki, et al.’s Introduction to Genetic Analysis, 7^th edition: “Mutation Breeding” (HTML)

Instructions: Please study this section on mutation breeding from Griffiths, Miller, Suzuki, et al.’s textbook.

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5.2.1 Reading: Dave’s Garden: LariAnn Garner’s “Totipotency—The Wonder of Stem Cells in Plants”

Link: Dave’s Garden: LariAnn Garner’s “Totipotency—The Wonder of Stem Cells in Plants” (HTML)

Instructions: Please study this page.

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5.2.2 Reading: University of Florida: Alba Myers’ “Somatic Embryogenesis Induction in Delonix Regia (Boger.) Raf (Royal Poinciana)”

Link: University of Florida: Alba Myers’ “Somatic Embryogenesis Induction in Delonix Regia (Boger.) Raf (Royal Poinciana)” (HTML)

Instructions: Please read this page, and identify examples of callus culture. Plant tissues are sterilized and placed on tissue culture medium, which induces “callus,” that is, undifferentiated cell formation.

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5.2.3 Reading: The University of New South Wales’ Cell Biology Wiki: Dr. Mark Hill’s “Group 4 Project—Cell Culture”

Link: The University of New South Wales’ Cell Biology Wiki: Dr. Mark Hill’s “Group 4 Project—Cell Culture” (HTML)

Instructions: Please study the “Harvesting and Isolating Cells” section on this page.

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5.3.1 Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Gelbart, Miller, et al.’s Modern Genetic Analysis: NCBI Bookshelf: Griffiths et al.’s “Recombinant DNA Technology in Eukaryotes”

Link: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Gelbart, Miller, et al.’s Modern Genetic Analysis: NCBI Bookshelf: Griffiths et al.’s “Recombinant DNA Technology in Eukaryotes” (HTML)

Instructions: Please study “The Ti plasmid” section on this page. The Ti plasmid is actually inserted by a bacteria species called Agrobacterium. Thus, when we talk about the Ti plasmid, we are referring to the plasmid inside Agrobacterium.

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5.3.2 Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Berg, et al.’s Biochemistry, 5th edition: “Manipulating the Genes of Eukaryotes”

Link: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Berg, et al.’s Biochemistry, 5^th edition: “Manipulating the Genes of Eukaryotes” (HTML)

Instructions: Please read the third and fourth paragraphs (starting with “Foreign DNA can be introduced . . . “) in the “6.3.6 Tumor-Inducing Plasmids Can Be Used to Introduce New Genes into Plant Cells” section.

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5.3.2 Reading: Saint John’s University: Stephen G. Saupe’s “Introduction to the Protoplast Lab”

Link: Saint John’s University: Stephen G. Saupe’s “Introduction to the Protoplast Lab” (HTML)

Instructions: Please study the “A Protoplast Primer” section on this page.

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5.3.2 Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Miller, Suzuki, et al.’s Introduction to Genetic Analysis, 7th edition: “Recombinant DNA Technology in Eukaryotes”

Link: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Miller, Suzuki, et al.’s Introduction to Genetic Analysis, 7^th edition: “Recombinant DNA Technology in Eukaryotes” (HTML)

Instructions: Please study the “Transgenic Eukaryotes” section on this page.

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5.4.1 Reading: University of Central Florida: Dheeraj Verma and Henry Daniell’s “Chloroplast Vector Systems for Biotechnology Applications”

Link: University of Central Florida: Dheeraj Verma and Henry Daniell’s “Chloroplast Vector Systems for Biotechnology Applications” (HTML or PDF)

Instructions: Please study the “Reporter Genes Used In Plastids” section on this page. You can access the PDF from the top right corner of the page.

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5.4.1 Reading: Wellesley College’s “?-Glucuronidase (GUS) Activity Assays of Transformed Plants”

Link: Wellesley College’s “β-Glucuronidase (GUS) Activity Assays of Transformed Plants” (HTML)

Instructions: Please study this page. Please note that β-glucuronidase is a reporter gene, which can be used to assess the succes of transformation.

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5.4.2 Reading: The Jackson Laboratory’s “Introduction to Cre-Lox Technology”

Link: The Jackson Laboratory’s “Introduction to Cre-Lox Technology” (HTML)

Instructions: Please study this page. Note that Cre-Lox Technology is used both on animals and plants.

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5.5.1 Reading: International Service for the Acquisition of Agri-Biotech Applications: “Pocket K No. 10: Herbicide Tolerance Technology: Glyphosate and Glufosinate”

Link: International Service for the Acquisition of Agri-Biotech Applications: “Pocket K No. 10: Herbicide Tolerance Technology: Glyphosate and Glufosinate” (HTML or PDF)

Instructions: Please study this page. You can access the PDF in various languages from the left-hand side of the page.

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5.5.2 Reading: John W. Kimball’s “Bacillus thuringiensis (Bt)”

Link: John W. Kimball’s “Bacillus thuringiensis (Bt)” (HTML)

Instructions: Please study this page.

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5.5.2 Reading: Nature Education’s Scitable: Losey et al.’s “Transgenic Pollen Harms Monarch Larvae”

Link: Nature Education’s Scitable: Losey et al.’s “Transgenic Pollen Harms Monarch Larvae” (PDF)

Instructions: Please study this publication in its entirety.

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5.5.3 Reading: Virginia Tech: Information Systems for Biotechnology: Teresa Capell’s “Enhanced Drought Tolerance In Transgenic Rice”

Link: Virginia Tech: Information Systems for Biotechnology: Teresa Capell’s “Enhanced Drought Tolerance In Transgenic Rice” (HTML)

Instructions: Please study this page. Author Theresa Chapel is from Department of Crop Genetics and Biotechnology, Schmallenberg, Germany.

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5.5.4 Reading: The NCAT Sustainable Agriculture Project’s “Transgenic Crops”

Link: The NCAT Sustainable Agriculture Project’s “Transgenic Crops” (HTML)

Instructions: Please study the “Crop Yield, Costs, and Profitability” section on this page.

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5.5.4 Reading: Nature Education’s Scitable: Leslie A. Pray’s “Quantitative Genetics: Growing Transgenic Tomatoes”

Link: Nature Education’s Scitable: Leslie A. Pray’s “Quantitative Genetics: Growing Transgenic Tomatoes” (HTML)

Instructions: Please study the entire article. Please note the similarities and differences between complex quantitative traits and single gene determined traits.

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5.5.5 Reading: International Service for the Acquisition of Agri-Biotech Applications: “Biotechnology and Biofortification”

Link: International Service for the Acquisition of Agri-Biotech Applications: “ Biotechnology and Biofortification” (HTML or PDF)

Instructions: Please read the content of this page. You can access the PDF from the left-hand side of the page.

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5.5.5 Reading: The American Society for Nutritional Sciences: The Journal of Nutrition: Bo Lönnerdal’s “Genetically Modified Plants for Improved Trace Element Nutrition”

Link: The American Society for Nutritional Sciences: The Journal of Nutrition: Bo Lönnerdal’s “Genetically Modified Plants for Improved Trace Element Nutrition” (HTML or PDF)

Instructions: Please study the “Insertion of Genes for Novel Metal-Binding Proteins” section on this page. You can access the PDF form from the right side of the page. Author Bo Lönnerdal works in the Department of Nutrition at the University of California. This is a peer-reviewed publication.

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5.6.1 Reading: Jim M. Dunwell’s “Transgenic Approaches to Crop Improvement”

Link: Jim M. Dunwell’s “Transgenic Approaches to Crop Improvement” (HTML or PDF)

Instructions: Please study the content of this page. You can access the PDF form on the righthand side of the page.

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5.6.1 Reading: John W. Kimball’s Biology Pages: “Arabidopsis Thaliana: Another ‘Model Organism’”

Links: John W. Kimball’s Biology Pages: “Arabidopsis Thaliana: Another ‘Model Organism’” (HTML)

Instructions: Please study this page. Please note that A. thaliana is the most widely used model organism in research aiming to produce new genetically modified plants.

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5.6.2 Reading: Oxford University Press’s Journal of Experimental Botony: Parry et al.’s “Mutation Discovery for Crop Improvement”

Link: Oxford University Press’s Journal of Experimental Botony: Parry et al.’s “Mutation Discovery for Crop Improvement” (HTML or PDF)

Instructions: Please study the “Introduction” and “Conclusions” sections on this page. You can access the PDF from the right side of the page. This is a peer-reviewed publication.

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5.6.3 Reading: Arizona Genomics Institute, Arizona Genomics Computational Laboratory, and Stanford University: “The Maize Full Length cDNA Project”

Link: Arizona Genomics Institute, Arizona Genomics Computational Laboratory, and Stanford University: “The Maize Full Length cDNA Project” (HTML)

Instructions: Please study the “Disrupt Gene Regulation: ‘Knockdown’ Technology” section on this page.

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5.7.1 Reading: National Education’s Scitable: Leslie A. Pray’s “Quantitative Genetics: Growing Transgenic Tomatoes”

Link: National Education’s Scitable: Leslie A. Pray’s “Quantitative Genetics: Growing Transgenic Tomatoes” (HTML)

Instructions: Please study the content of this page. Longer shelf life, size, and taste are some of the traits that are targeted in transgenic tomatoes. Please note the broad range of traits, which transgenic technology attempts to modify.

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5.7.2 Reading: National Center for Biotechnology Information: The Yonsei University’s College of Medicine: Yonsei Medical Journal: Sang-Ha Kim, et al.’s “Evaluating the Allergic Risk of Genetically Modified Soybean”

Link: National Center for Biotechnology Information: The Yonsei University’s College of Medicine: Yonsei Medical Journal: Sang-Ha Kim, et al.’s “Evaluating the Allergic Risk of Genetically Modified Soybean” (HTML or PDF)

Instructions: Please study the “Introduction” and “Discussion” sections on this page. You can access the PDF form from the top left corner of the page. This is a peer-reviewed publication. Please note that possible allergic reaction to transgenic soybean is discussed.

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5.7.3 Reading: PLoS Biology: Virginia Gewin's “Genetically Modified Corn— Environmental Benefits and Risks”

Link: PLoS Biology: Virginia Gewin's “Genetically Modified Corn— Environmental Benefits and Risks” (HTML or PDF)

Instructions: Please study this page. You can download this material in PDF form from the top right corner of the page. Protection from insect pests was a major driving force of transgenic corn development. Please note the environmental risk of decreasing diversity. Author Gewin is a freelance science journalist.

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5.7.4 Reading: Plant Management Network: Dennis Gonsalves and Steve Ferreira’s “Transgenic Papaya: A Case for Managing Risks of Papaya Ringspot Virus in Hawaii”

Link: Plant Management Network: Dennis Gonsalves and Steve Ferreira’s “Transgenic Papaya: A Case for Managing Risks of Papaya Ringspot Virus in Hawaii” (HTML)

Instructions: Please study this page. Protection from viral infection was the major driving force of transgenic papaya development. Please note the impact of the transgenic plant on the cultivation of nontransgenic papaya in the virus infected area.

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5.7.5 Reading: GMO Compass: “Rice”

Link: GMO Compass: “Rice” (HTML)

Instructions: Please study this page. Please note that golden rice is an example of improved nutritional value of a genetically modified plant.

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5.8.1 Reading: Ohio State University: Dresbach et al.’s “The Impact of Genetically Modified Organisms on Human Health”

Link: Ohio State University: Dresbach et al.’s “The Impact of Genetically Modified Organisms on Human Health” (HTML or PDF)

Instructions: Please study this page. You can access the PDF at the bottom of the page.

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5.8.2 Reading: Emory University’s “GMO and Environment: Once a Gene’s In, Where Does It Go?”

Link: Emory University’s “GMO and Environment: Once a Gene’s In, Where Does It Go?” (HTML)

Instructions: Please study this page. Please note that a decreasing diversity makes species more vulnerable to environmental changes.

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6.1 Reading: Nature Education’s Scitable: Leslie Pray’s “Recombinant DNA Technology and Transgenic Animals”

Link: Nature Education’s Scitable: Leslie Pray’s “Recombinant DNA Technology and Transgenic Animals” (HTML)

Instructions: Please study this page. Dr. Pray gives an overview on the making of transgenic animals.

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6.1 Reading: Wellcome Trust: Richard Twyman’s “Transgenic Mice”

Link: Wellcome Trust: Richard Twyman’s “Transgenic Mice” (HTML)

Instructions: Please study this page including the slide show.

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6.2.1 Reading: John W. Kimball’s Biology Pages: “Genetic Mosaics”

Link: John W. Kimball’s Biology Pages: “Genetic Mosaics” (HTML)

Instructions: Please study this page. Please note that chimeras can be considered as paternal twins living in one body. Chimeric individuals may look and function perfectly normal and may stay unnoticed unless genetic testing is performed on their different body parts.

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6.2.2 Reading: Kenyon College: Dr. Wade Powell’s “Differential Gene Expression and Development”

Link: Kenyon College: Dr. Wade Powell’s “Differential Gene Expression and Development” (HTML)

Instructions: Please study this page. Please note that differential gene expression may result in cell differentiation without the loss of genetic information in the differentiated cell.

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6.2.3 Reading: Case Western Reserve University’s “Targeting Vector Design”

Link: Case Western Reserve University’s “Targeting Vector Design” (HTML)

Instructions: Please study the content of this page.

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6.2.4 Reading: National Center for Biotechnology Information’s PubMed: Society for Endocrinology's Journal of Endocrinology: Ryding, et al.’s “Conditional Transgenic Technologies”

Link: National Center for Biotechnology Information’s PubMed: Society for Endocrinology's Journal of Endocrinology: Ryding, et al.’s “Conditional Transgenic Technologies” (PDF)

Instructions: Please click on “Society for Endocrinology Free Full Text” (in blue box, right top side of the page under PubMed.gov heading), and download the full publication as a PDF. Study the entire publication. The authors work at the University of Edinburgh, UK. This is a peer-reviewed publication.

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6.3.1 Reading: Nature Education’s Scitable: “Scientists Can Analyze Gene Function by Deleting Gene Sequences”

Link: Nature Education’s Scitable: “Scientists Can Analyze Gene Function by Deleting Gene Sequences” (HTML)

Instructions: Please study this page. Knockout mice refer to mice that have a selected gene intentionally silenced or removed.

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6.3.1 Reading: Nature Education’s Scitable: “Transgenic Animals Have Genomes That Have Been Permanently Altered Through Recombinant DNA Technology.”

Link: Nature Education’s Scitable: “Transgenic Animals Have Genomes That Have Been Permanently Altered Through Recombinant DNA Technology.” (HTML)

Instructions: Please study the diagram.

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6.3.1 Reading: Nature Education’s Scitable: John Sterling’s “Gene Therapy Restores Vision to Mice”

Link: Nature Education’s Scitable: John Sterling’s “Gene Therapy Restores Vision to Mice” (Adobe Flash)

Instructions: Please listen to the audio (10 minutes). Knockin mice refer to mice that have a specific gene intentionally added.

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6.3.2 Reading: National Center for Biotechnology Information’s Bookshelf: CRC Press: Rodriguiz and Wetsel’s Animal Models of Cognitive Impairment: “Chapter 12: Assessments of Cognitive Deficits in Mutant Mice”

Link: National Center for Biotechnology Information’s Bookshelf: CRC Press: Rodriguiz and Wetsel’s Animal Models of Cognitive Impairment: “Chapter 12: Assessments of Cognitive Deficits in Mutant Mice” (HTML)

Instructions: Please study this entire chapter from Levin and Buccafusco (ed.)’s Animal Models of Cognitive Impairment. The authors are affiliated with Duke University’s Medical Center.

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6.4.1 Reading: The Company of Biologists’ Development: Venken and Bellen’s “Transgenesis Upgrades for Drosophila melanogaster”

Link: The Company of Biologists’ Development: Venken and Bellen’s “Transgenesis Upgrades for Drosophila melanogaster” (HTML or PDF)

Instructions: Please study the following sections: “Summary,” “Introduction,” “Fig.1 Drosophila Transgenesis,” “Box 4. Site-Specific Recombinases and Integrases,” and “Future Applications.” You can access the PDF from the right-hand side of the page.

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6.4.2 Reading: Wiley Online Library: Yamamoto, et al.’s “ Flying Vaccinator; a Transgenic Mosquito Delivers a Leishmania Vaccine via Blood Feeding”

Link: Wiley Online Library: Yamamoto, et al.’s “Flying Vaccinator; a Transgenic Mosquito Delivers a Leishmania Vaccine via Blood Feeding” (HTML or PDF)

Instructions: Please study the “Abstract,” “Introduction,” “Generation of Transgenic Lines,” and “Antibody Responses to mDsRed-SP15 in Mice Exposed to Transgenic Mosquitoes” sections on this page. You can access the PDF for the right-hand side of the page under “Article Tools.” The authors work in the Department of Infection and Immunity at the Jichi Medical University, Japan. This is a peer-reviewed publication.

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6.5.1 Reading: National Center for Biotechnology Information’s Bookshelf: Wiley-Liss: Strachan and Read’s Human Molecular Genetics, 2nd edition: “Chapter 21: Genetic Manipulation of Animals”

Link: National Center for Biotechnology Information’s Bookshelf: Wiley-Liss: Strachan and Read’s Human Molecular Genetics, 2^nd edition: “Chapter 21: Genetic Manipulation of Animals” (HTML)

Instructions: Please study “Manipulating Animals by Somatic Cell Nuclear Transfer” on this page, including the “Principles and Practice of Animal Cloning” and “The Successful Cloning of an Adult Animal Has Major Implications for Research, Medicine and Society” sections.

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6.5.1 Reading: National Center for Biotechnology Information’s PubMed: Canadian Medical Association Journal: Leigh Turner’s “A Sheep Named Dolly”

Link: National Center for Biotechnology Information’s PubMed: Canadian Medical Association Journal: Leigh Turner’s “A Sheep Named Dolly” (PDF)

Instructions: Please study this publication. Click on PDF under the title to download the full text. Author Turner works at the Hastings Center.

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6.5.2 Reading: Nature Education’s Scitable: Swanson et al.’s “Extraordinary Salmon Growth”

Link: Nature Education’s Scitable: Swanson et al.’s “Extraordinary Salmon Growth” (PDF)

Instructions: Please study this entire paper. The authors work at Harvard Medical School.

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6.5.3 Reading: National Center for Biotechnology Information’s PubMed: Reproductive Biology and Endocrinology: Jie Xu and Xiangzhong Yang’s “Will Cloned Animals Suffer Premature Aging—The Story at the End of Clones’ Chromosomes”

Link: National Center for Biotechnology Information’s PubMed: Reproductive Biology and Endocrinology: Jie Xu and Xiangzhong Yang’s “Will Cloned Animals Suffer Premature Aging—The Story at the End of Clones’ Chromosomes” (HTML or PDF)

Instructions: Please study the content of this page. You can access the PDF from the top right corner of the page. This is a peer-reviewed publication.

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6.6.1 Reading: John W. Kimball’s Biology Pages: “Transgenic Animals”

Link: John W. Kimball’s Biology Pages: “Transgenic Animals” (HTML)

Instructions: Please read the “Transgenic Sheep and Goats” and “Transgenic Chickens” sections on this page.

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6.6.1 Reading: Iowa State University: David F. Betsch’s “Pharmaceutical Production from Transgenic Animals”

Link: Iowa State University: David F. Betsch’s “Pharmaceutical Production from Transgenic Animals” (HTML)

Instructions: Please study this page.

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6.6.2 Reading: John W. Kimball’s Biology Pages: “Organ Transplants”

Link: John W. Kimball’s Biology Pages: “Organ Transplants” (HTML)

Instructions: Please read starting with “What are the future prospects for transplantation?” to the end this page.

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6.7.1 Reading: Nature Education’s Scitable: Leslie A. Pray’s “Embryo Screening and the Ethics of Human Genetic Engineering”

Link: Nature Education’s Scitable: Leslie A. Pray’s “Embryo Screening and the Ethics of Human Genetic Engineering” (HTML)

Instructions: Please study this page. Dr. Pray reviews opposing opinions and recent practice on preimplantation genetic diagnosis. She is challenging you by asking "What do you think?:" should we improve human genome, or should we focus on the danger of misuse?

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6.7.2 Reading: Sierra Club’s “Genetic Engineering at a Historic Crossroads”

Link: Sierra Club’s “Genetic Engineering at a Historic Crossroads” (HTML)

Instructions: Please read “Historic turning point.”

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6.7.3 Reading: MIT’s Technology Review: Emily Singer’s “The Dark Side of Pet Cloning”

Link: MIT’s Technology Review: Emily Singer’s “The Dark Side of Pet Cloning” (HTML)

Instructions: Please study this page. Please note that genetically identical animals have different personalities, just like identical twins.

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6.7.4 Reading: KAC’s version of Jeremy Manier’s “Art Takes a Genetic Engineering Leap”

Link: KAC’s version of Jeremy Manier’s “Art Takes a Genetic Engineering Leap” (HTML)

Instructions: Please read this page. This article was originally published in the Chicago Tribune on September 19, 2000.

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6.7.5 Reading: University of Hawaii, Honolulu: Professor Ronald C. Pine’s version of Bob Sullivan’s “Religious Views of Cloning Do Not Agree”

Link: University of Hawaii, Honolulu: Professor Ronald C. Pine’s version of Bob Sullivan’s “Religious Views of Cloning Do Not Agree” (HTML)

Instructions: Please read this page.

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7.1.1 Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Gelbart, Miller, et al.’s Modern Genetic Analysis: “Changes in Chromosome Number”

Link: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman:Griffiths, Gelbart, Miller, et al.’s Modern Genetic Analysis: “Changes in Chromosome Number” (HTML)

Instructions: Please study the content of the “Aneuploidy” section, including the “Nondisjunction,” “Monosomics (2 - 1),” and “Trisomics (2n + 1)” subsections on this page.

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7.1.2 Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Gelbart, Miller, et al.’s Modern Genetic Analysis: “Chromosomal Rearrangements”

Link: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Gelbart, Miller, et al.’s Modern Genetic Analysis: “Chromosomal Rearrangements” (HTML)

Instructions: Please study this page.

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7.1.3 Reading: Nature Education’s Scitable: Danielle Simmons’ “Epigenetic Influences and Disease”

Link: Nature Education’s Scitable: Danielle Simmons’ “Epigenetic Influences and Disease” (HTML)

Instructions: Please study this page. Epigenetics is "in addition to" genetics. Please note that epigenetic changes result in gene expression changes without changing the sequence of the genomic DNA. Identical twins may be susceptible to different diseases, if their epigenetics are different due to different life style.

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7.2.1 Reading: Nature Education’s Scitable: Abram Gabriel and Jennifer Przybylski’s “Sickle-Cell Anemia: A Look at Global Haplotype Distribution”

Link: Nature Education’s Scitable: Abram Gabriel and Jennifer Przybylski’s “Sickle-Cell Anemia: A Look at Global Haplotype Distribution” (HTML)

Instructions: Please study the content of this page. Authors Gabriel and Przybylski work at the Rutgers University. Please note the advantage, what the deadly sickle-cell anemia provides for heterozygous individuals.

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7.2.2 Reading: National Human Genome Research Institute’s “Learning about Cystic Fibrosis”

Link: National Human Genome Research Institute’s “Learning about Cystic Fibrosis” (HTML)

Instructions: Please study the content of this page.

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7.2.3 Reading: National Center for Biotechnology Information’s PubMed: Blackwell Publishing Ltd.'s British Journal of Haematology: Samuel L. Murphy and Katherine A. High’s “Gene Therapy for Haemophilia”

Link: National Center for Biotechnology Information’s PubMed: Blackwell Publishing Ltd.'s British Journal of Haematology: Samuel L. Murphy and Katherine A. High’s “Gene Therapy for Haemophilia” (HTML or PDF)

Instructions: Please study the content of this page. You can access the PDF from the top right corner of the page. The authors work in the Department of Pediatrics at the Children's Hospital of Philadelphia. This is a peer-reviewed publication.

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7.2.4 Reading: National Center for Biotechnology Information’s “Phenylketonuria”

Link: National Center for Biotechnology Information’s “Phenylketonuria” (HTML)

Instructions: Please study the content of this page. Please note that phenylalanine is an essential amino acid, thus it can not be omitted entirely from the diet.

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7.2.5 Reading: National Center for Biotechnology Information’s “Duchenne Muscular Dystrophy”

Link: National Center for Biotechnology Information’s “Duchenne Muscular Dystrophy” (HTML or PDF)

Instructions: Please study the table on this page. Please note that Duchenne muscular dystrophies are X-linked, thus the disease is more common in males.

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7.2.6 Reading: Nature Education’s Scitable: Heidi Chial’s “Huntington’s Disease: The Discovery of the Huntingtin Gene”

Link: Nature Education’s Scitable: Heidi Chial’s “Huntington’s Disease: The Discovery of the Huntingtin Gene” (HTML)

Instructions: Please study this page. More than 40 CAG nucleotide repeat in the HTT gene is linked to the onset of Huntington’s disease.

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7.2.6 Reading: National Center for Biotechnology Information’s “Fragile X Syndrome

Link: National Center for Biotechnology Information’s “Fragile X Syndrome” (HTML or PDF)

Instructions: Please study the content of this page. Fragile X syndrome is the most common inherited mental retardation. It is an X-linked condition. Please note that the chromosome becomes fragile only during a staining procedure; it is not fragile in the cell. More than 200 CGG nucleotide repeat in the fragile X gene causes the disease.

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7.3 Reading: Nature Education’s Scitable: Karen E. Norrgard’s “Genetic Counseling: Genetic Testing, Family History and Psychosocial Evaluation”

Link: Nature Education’s Scitable: Karen E. Norrgard’s “Genetic Counseling: Genetic Testing, Family History and Psychosocial Evaluation” (HTML)

Instructions: Please study the three case studies on this page.

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7.3 Reading: Nature Education’s Scitable: Karen Norrgard’s “Diagnosing Down Syndrome, Cystic Fibrosis, Tay-Sachs Disease and Other Genetic Disorders”

Link: Nature Education’s Scitable: Karen Norrgard’s “Diagnosing Down Syndrome, Cystic Fibrosis, Tay-Sachs Disease and Other Genetic Disorders” (HTML)

Instructions: Please study the content of this page. Dr. Norrgard reviews genetic screening in the newborn, during pregnancy and before implantation.

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7.4.1 Reading: Nature Education’s Scitable: Heidi Chial’s “Gene-Based Therapeutic Approaches”

Link: Nature Education’s Scitable: Heidi Chial’s “Gene-Based Therapeutic Approaches” (HTML)

Instructions: Please learn content from the “Putting the Human Genome to Work: Using Genes to Treat Disease” section to the end of this page.

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7.4.2 Reading: National Center for Biotechnology Information’s Bookshelf: Strachan and Read's "Human Molecular Genetics": "Chapter 22: Gene Therapy and Other Molecular Genetic-Based Therapeutic Approaches"

Link: National Center for Biotechnology Information’s Bookshelf: Strachan and Read's "Human Molecular Genetics:” "Chapter 22: Gene Therapy and Other Molecular Genetic-Based Therapeutic Approaches" (HTML)

Instructions: Please scroll down to and read section 22.2: “The Technology of Classical Gene Therapy.”

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7.4.3 Reading: American Society for Clinical Investigation's The Journal of Clinical Investigation: Caroline J. Springer and Ion Niculescu-Duvaz’s “Prodrug-Activating Systems in Suicide Gene Therapy”

Link: American Society for Clinical Investigation's The Journal of Clinical Investigation: Caroline J. Springer and Ion Niculescu-Duvaz’s “Prodrug-Activating Systems in Suicide Gene Therapy” (HTML or PDF)

Instructions: Please study the introduction, “Parameters that influence the success of GDEPT systems,” and “Future perspectives” sections. You can access the PDF under “article tools” on the left-hand side of the page. The authors work in the Cancer Research Campaign Centre for Cancer Therapeutics at the Institute of Cancer Research, Sutton, Surrey, UK.

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7.5.1 Reading: John W. Kimball’s Biology Pages: “Gene Therapy II”

Link: John W. Kimball’s Biology Pages: “Gene Therapy II” (HTML)

Instructions: Please study this page.

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7.5.2 Reading: Genetherapynet.com’s “Retroviral Vectors”

Link: Genetherapynet.com’s “Retroviral Vectors” (HTML or PDF)

Instructions: Please study this page. You can access the PDF by clicking on the Adobe icon at the top of the page.

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7.5.3 Reading: Davidson College: Megan McDonald’s “Gene Guns”

Link: Davidson College: Megan McDonald’s “Gene Guns” (HTML)

Instructions: Please study this page.

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7.5.4 Reading: University of Pennsylvania’s Diamond Lab: “Gene Therapy”

Link: University of Pennsylvania’s Diamond Lab: “Gene Therapy” (HTML)

Instructions: Please study this page.

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7.5.5 Reading: Thomas Jefferson University’s “Laboratory of Nucleic Acid Therapeutics”

Link: Thomas Jefferson University’s “Laboratory of Nucleic Acid Therapeutics” (HTML)

Instructions: Please read this page.

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7.6.1 Reading: John W. Kimball’s Biology Pages: “Gene Therapy I”

Link: John W. Kimball’s Biology Pages: “Gene Therapy I” (HTML)

Instructions: Please study this page.

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7.6.2 Reading: Gene Therapy Review: Christophe Pichavant’s “Gene Therapy for Duchenne Muscular Dystrophy”

Link: Gene Therapy Review: Christophe Pichavant’s “Gene Therapy for Duchenne Muscular Dystrophy” (HTML)

Instructions: Please study the entire article.

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7.6.3 Reading: PLOS Pathogens: Wilen et al’s “Engineering HIV-Resistant Human CD4+ T Cells with CXCR4-Specific Zinc-Finger Nucleases”

Link: PLOS Pathogens: Wilen et al’s “Engineering HIV-Resistant Human CD4+ T Cells with CXCR4-Specific Zinc-Finger Nucleases” (HTML or PDF)

Instructions: Please study the “Abstract,” “Author Summary,” and “Introduction” sections. You can download the PDF from the top right corner of the page. This is a peer-reviewed publication.

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8.1.1 Reading: Stanford University: Phillip Thurtle’s “The Creation of Genetic Identity”

Link: Stanford University: Phillip Thurtle’s “The Creation of Genetic Identity” (HTML)

Instructions: Please study “Budding Concerns: The Creation of Genetic Identity” on this page.

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8.1.2 Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “DNA Forensics”

Link: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “DNA Forensics” (HTML)

Instructions: Please study this page.

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8.1.3 Reading: Nature Education’s Scitable: Karen Norrgard’s “Forensics, DNA Fingerprinting, and CODIS”

Link: Nature Education’s Scitable: Karen Norrgard’s “Forensics, DNA Fingerprinting, and CODIS” (HTML)

Instructions: Please study the content of this page. Please note that FBI is using STR sequences from 13 noncoding regions for the identification of individuals; the amelogenin gene is used additionally for gender determination.

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8.1.3 Reading: FBI’s “CODIS Core STR Loci”

Link: FBI’s “CODIS Core STR Loci” (HTML)

Instructions: Please study the content of this page. Please note that the STR repeats are used from different chromosomes. "AMEL" stands for the amelogenin gene, and it is used for sex-typing.

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8.2 Reading: Nature Education’s Scitable: Leslie A. Pray’s “Legislative Landmarks of Forensics: California v. Greenwood and Shed DNA”

Link: Nature Education’s Scitable: Leslie A. Pray’s “Legislative Landmarks of Forensics: California v. Greenwood and Shed DNA” (HTML)

Instructions: Please read the content of this page. Please note that the 13 STRs that are currently used for DNA profiling do not reveal medical information.

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8.3 Reading: Nature Education’s Scitable: Jill Adams’ “Paternity Testing: Blood Types and DNA”

Link: Nature Education’s Scitable: Jill Adams’ “Paternity Testing: Blood Types and DNA” (HTML)

Instructions: Please study the content of this page. Please note that blood typing is a good and inexpensive starting point in paternity cases. DNA fingerprinting can be used for high accuracy result.

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8.4.1 Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “DNA Forensics”

Link: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “DNA Forensics” (HTML)

Instructions: Please study the “Mitochondrial DNA Analysis” section on this page. Please note that mitochondrial DNA is maternally inherited; a mother and her children all have identical mitochondrial DNA. Thus, mitochondrial DNA is not individual. On the other hand, it is present in many copies in a cell, which offers higher sensitivity. Higher sensitivity is crucial, when samples are decayed. Forensic mitochondrial DNA analysis is more elaborate, because it involves sequencing and sequence analysis of the samples.

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8.4.2 Reading: Science Spectra: Neil Bradman and Mark Thomas’ “Why Y?”

Link: Science Spectra: Neil Bradman and Mark Thomas’ “Why Y?” (HTML)

Instructions: Please study this page. Please note that human Y chromosome is paternally inherited. Males in one paternal lineage have identical Y chromosomes.

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8.5.1 Reading: Michigan State University: Salil Prabhakar and Anil Jain’s “Fingerprint Identification”

Link: Michigan State University: Salil Prabhakar and Anil Jain’s “Fingerprint Identification” (HTML)

Instructions: Please study this page. Please note that friction ridge pattern analysis is a pattern analysis that is not fully computerized. Thus, it requires the opinion of experts.

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8.5.2 Reading: John Daugman’s “Iris Recognition”

Link: John Daugman’s “Iris Recognition” (HTML)

Instructions: Please study this page.

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9.1.1 Reading: Kenneth Todar’s Online Textbook of Bacteriology: “The Impact of Microbes on the Environment and Human Activities”

Links: Kenneth Todar’s Online Textbook of Bacteriology: “The Impact of Microbes on the Environment and Human Activities” (HTML)

Instructions: Please study all four pages. Use the “next page” or “chapter continued” buttons at the bottom of the page to access pgs 2-4.

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9.1.2 Reading: MIT’s Biological Energy Interest Group: Weigele’s “Biology of Hydrogen Production”

Links: MIT’s Biological Energy Interest Group: Weigele’s “Biology of Hydrogen Production” (HTML)

Instructions: Please study the content of this page.

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9.1.3 Reading: University of South Carolina, School of Medicine’s Microbiology and Immunology Online: Alvin Fox’s “Bacteriology—Chapter Three: Nutrition, Growth and Energy Metabolism”

Links: University of South Carolina, School of Medicine’s Microbiology and Immunology Online: Alvin Fox’s “Bacteriology—Chapter Three: Nutrition, Growth and Energy Metabolism” (HTML)

Instructions: Please study this page.

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9.1.4 Reading: National Center for Biotechnology Information’s Bookshelf: ASM Press: David R. Drake and Kim A. Brogden’s Polymicrobial Diseases: “Continuous-Culture Chemostat Systems and Flowcells as Methods to Investigate Microbial Interactions”

Links: National Center for Biotechnology Information’s Bookshelf: ASM Press: David R. Drake and Kim A. Brogden’s Polymicrobial Diseases: “Continuous-Culture Chemostat Systems and Flowcells as Methods to Investigate Microbial Interactions” (HTML)

Instructions: Please study this page.

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9.2 Reading: BioMed Central: Microbial Cell Factories: Nasib Qureshi et al.’s “Biofilm Reactors for Industrial Bioconversion Processes: Employing Potential of Enhanced Reaction Rates”

Link: BioMed Central: Microbial Cell Factories: Nasib Qureshi et al.’s “Biofilm Reactors For Industrial Bioconversion Processes: Employing Potential of Enhanced Reaction Rates” (HTML or PDF)

Instructions: Please study the content of this page. You can access the PDF under “viewing options” on the right-hand side of the page. This is a peer-reviewed publication.

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9.3.1 Reading: The Samuel Roberts Noble Foundation’s “What Does Organic Matter Do In Soil?”

Link: The Samuel Roberts Noble Foundation’s “What Does Organic Matter Do In Soil?” (HTML)

Instructions: Please study the content of this page.

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9.3.2 Reading: Province of British Columbia: Ministry of Agriculture’s “Environmental Protection”

Link: Province of British Columbia: Ministry of Agriculture’s “Environmental Protection” (HTML)

Instructions: Please study this page.

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9.3.3 Reading: National Center for Biotechnology Information’s PubMed: American Society for Microbiology: Microbiological Reviews: Leahy and Colwell’s “Microbial Degradation of Hydrocarbons in the Environment”

Link: National Center for Biotechnology Information’s PubMed: American Society for Microbiology: Microbiological Reviews: Leahy and Colwell’s “Microbial Degradation of Hydrocarbons in the Environment” (PDF)

Instructions: In order to access the full manuscript, follow the directions under “Full Text” heading. Please study the full text. The authors work in the Department of Microbiology at the University of Maryland.

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9.3.4 Reading: Green Footsteps’ “Industrial Pollution Causes Land Pollution”

Link: Green Footsteps’ “Industrial Pollution Causes Land Pollution” (HTML)

Instructions: Please study this page.

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9.3.5 Reading: Federal Remediation Technologies Roundtable’s “In Situ Biological Treatment for Soil, Sediment, Bedrock and Sludge”

Link: Federal Remediation Technologies Roundtable’s “In Situ Biological Treatment for Soil, Sediment, Bedrock and Sludge” (HTML)

Instructions: Please study this page.

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9.3.5 Reading: Federal Remediation Technologies Roundtable’s “Ex Situ Biological Treatment for Soil, Sediment, Bedrock and Sludge”

Link: Federal Remediation Technologies Roundtable’s “Ex Situ Biological Treatment for Soil, Sediment, Bedrock and Sludge” (HTML)

Instructions: Please study this page.

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9.4.1 Reading: United States Environmental Protection Agency’s “What Are the Six Common Air Pollutants?”

Link: United States Environmental Protection Agency’s “What Are the Six Common Air Pollutants?” (HTML)

Instructions: Please read this page, and follow these links to learn about common air pollutants: “Ozone,” “Particulate Matter,” “Carbon Monoxide,” “Nitrogen Oxide,” “Sulfur Dioxide,” “Lead,” “Latest Findings on National Air Quality: Status and Trends,” and within it the air pollutants link; furthermore, please follow all links under the “Health Effects Information” heading.

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9.4.2 Reading: Green Solutions Magazine: Maggie Romuld’s “Using Bio-Oxidation to Prevent Air Pollution”

Link: Green Solutions Magazine: Maggie Romuld’s “Using Bio-Oxidation to Prevent Air Pollution” (HTML)

Instructions: Please study the content of this page.

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9.4.3 Reading: Rensselaer Polytechnic Institute: Selvi B. Anit and Robert J. Artuz’s “Biofiltration of Air”

Link: Rensselaer Polytechnic Institute: Selvi B. Anit and Robert J. Artuz’s “Biofiltration of Air” (HTML)

Instructions: Please study this page.

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9.5.1 Reading: Texas A & M University: Robert Stewards’s “Groundwater Contamination”

Link: Texas A & M University: Robert Stewards’s “Groundwater Contamination” (HTML)

Instructions: This page summarizes contaminants and it also outlines activities that lead to groundwater contamination. Please study the entire page.

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9.5.1 Reading: Texas A & M University: Robert Stewart’s “Environmental Science in the 21st Century - Ground Water Contamination”

Link: Texas A & M University: Robert Stewart’s “Environmental Science in the 21st Century - Ground Water Contamination” (HTML)

Instructions: Please study the content of this page for an overview on ground water contamination.

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9.5.2 Reading: Federal Remediation Technologies Roundtable’s “Ex Situ Biological Treatment for Groundwater, Surface Water, and Leachate”

Link: Federal Remediation Technologies Roundtable’s “Ex Situ Biological Treatment for Groundwater, Surface Water, and Leachate” (HTML)

Instructions: Please study the content of this page.

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9.5.3 Reading: United States Environmental Protection Agency’s “In-Situ Groundwater Bioremediation”

Link: United States Environmental Protection Agency’s “In-Situ Groundwater Bioremediation” (HTML)

Instructions: Please study the content of this page.

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9.5.4 Reading: Center for Public Environmental Oversight’s “Bio-Reactors”

Link: Center for Public Environmental Oversight’s “Bio-Reactors” (HTML)

Instructions: Please study this page.

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9.6.1 Reading: United States Department of Agriculture’s “Phytoremediation: Using Plants to Clean Up Soils”

Link: United States Department of Agriculture’s “Phytoremediation: Using Plants to Clean Up Soils” (HTML)

Instructions: Please study this page.

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9.6.2 Reading: Environmental Thinking: Tony Kobilnyk’s “Energy Savings Using Membrane Bioreactor Technology"

Link: Environmental Thinking: Tony Kobilnyk’s “Energy Savings Using Membrane Bioreactor Technology” (HTML)

Instructions: Please study this page.

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9.7.1 Reading: Marietta College: Dave McShaffrey’s “Bioaccumulation & Biomagnification”

Link: Marietta College: Dave McShaffrey’s “Bioaccumulation & Biomagnification” (HTML)

Instructions: Please study the content of the “Heavy Metals and Other Substances” section on this page.

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9.7.2 Reading: Universidad Católica de Valparaíso, Chile's Electronic Journal of Biotechnology: Fernando Acevedo’s “Present and Future of Bioleaching in Developing Countries”

Link: Universidad Católica de Valparaíso, Chile'sElectronic Journal of Biotechnology: Fernando Acevedo’s “Present and Future of Bioleaching in Developing Countries” (HTML or PDF)

Instructions: Please study this page. You can access the PDF by clicking the “Reprint (PDF) link above the Abstract.

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9.7.3 Reading: Microbiology: Geoffrey Michael Gadd’s “Metals, Minerals and Microbes: Geomicrobiology and Bioremediation”

Link: Microbiology: Geoffrey Michael Gadd’s “Metals, Minerals and Microbes: Geomicrobiology and Bioremediation” (HTML or PDF)

Instructions: Please study the “Metal Mobilization” and “Metal Immobilization” sections on this page. You can access the PDF format in the right-hand side of the page. Author Gadd works in the Division of Molecular Microbiology, College of Life Sciences at the University of Dundee, UK. This is a peer-reviewed publication.

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9.7.4 Reading: Society for General Microbiology's Microbiology: Geoffrey Michael Gadd’s “Metals, Minerals and Microbes: Geomicrobiology and Bioremediation”

Link: Society for General Microbiology's Microbiology: Geoffrey Michael Gadd’s “Metals, Minerals and Microbes: Geomicrobiology and Bioremediation” (HTML or PDF)

Instructions: Please study the “Reductive Transformations, Nanoparticle Formation and Nano-Biotechnology” section on this page. You can access the PDF format in the right-hand side of the page. Author Gadd works in the Division of Molecular Microbiology, College of Life Sciences at the University of Dundee, UK. This is a peer-reviewed publication.

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9.8.1 Reading: Wikipedia’s “Alcohol Fuel”

Link: Wikipedia’s “Alcohol Fuel” (PDF)

Instructions: Please study this page. Please note that not all alternative fuels are produced without using microorganisms; for example, esterification, a chemical reaction, is used to make biodiesel, and fractional distillation, a physical method, is employed to make green diesel. Methods that do not use living organisms for production are not covered in this course.

Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0 (HTML). You can find the original Wikipedia version of this article here (HTML).

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9.8.3 Reading: National Center for Biotechnology Information’s PubMed: Springer: Photosynthesis Research: Hemschemeier et al.’s “Analytical Approaches to Photobiological Hydrogen Production in Unicellular Green Algae”

Link: National Center for Biotechnology Information’s PubMed: Springer: Photosynthesis Research: Hemschemeier et al.’s “Analytical Approaches to Photobiological Hydrogen Production in Unicellular Green Algae” (HTML)

Instructions: Please study this publication, because it explains several approaches for biohydrogen production. Please note that genetically engineered microorganisms are in the focus of biohydrogen production. This is a peer-reviewed publication.

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9.8.4 Reading: MIT’s Technology Review: Kevin Bullis’s “Fuel from Algae”

Link: MIT’s Technology Review: Kevin Bullis’s “Fuel from Algae” (HTML)

Instructions: Please study this page. Note that genetically engineered algae is used to make oil.

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10.1.1 Reading: Wikipedia’s “Nanobiotechnology”

Link: Wikipedia’s “Nanobiotechnology” (PDF)

Instructions: Please study the content of this page.

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10.1.2 Reading: Nanoscience’s “Atomic Force Microscopy”

Link: Nanoscience’s “Atomic Force Microscopy” (HTML)

Instructions: Please study this page.

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10.1.3 Reading: National Center for Biotechnology Information’s PubMed: Dove Medical Press Limited: Wim De Jong and Paul Borm’s “Drug Delivery and Nanoparticles: Applications and Hazards”

Link: National Center for Biotechnology Information’s PubMed: Dove Medical Press Limited: Wim De Jong and Paul Borm’s “Drug Delivery and Nanoparticles: Applications and Hazards” (HTML or PDF)

Instructions: Please study the content of this page. You can access the PDF from the top right corner of the page. This is a peer-reviewed publication.

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10.1.4 Reading: Nano Science and Technology Institute: Srinivas Iyer, et al.’s “Biomolecular Motors”

Link: Nano Science and Technology Institute: Srinivas Iyer, et al.’s “Biomolecular Motors” (HTML)

Instructions: Please study the content of this page.

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10.1.5 Reading: Oak Ridge National Laboratory’s “Nanosensor Probes Single Living Cells”

Link: Oak Ridge National Laboratory’s “Nanosensor Probes Single Living Cells” (HTML)

Instructions: Please study this page.

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10.2 Reading: Federation of American Scientists’ “Introduction to Biological Weapons”

Link: Federation of American Scientists’ “Introduction to Biological Weapons” (HTML)

Instructions: Please study this page.

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10.3.1 Reading: Davidson College: Department of Biology’s “Monoclonal Antibodies”

Link: Davidson College: Department of Biology’s “Monoclonal Antibodies” (HTML)

Instructions: Please study this page.

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10.3.2 Reading: National Center for Biotechnology Information’s PubMed: e-Century Publishing Corporation's American Journal of Translational Research: Peter D. Burbelo et al.’s “Synthetic Biology for Translational Research”

Link: National Center for Biotechnology Information’s PubMed: e-Century Publishing Corporation's American Journal of Translational Research: Peter D. Burbelo et al.’s “Synthetic Biology for Translational Research” (HTML or PDF)

Instructions: Please study the “Synthetic Biology for Immunoassay Diagnostics” section on this page. You can access the PDF from the top right corner of the page. The authors work at the National Institute of Health, Bethesda. This is a peer-reviewed publication.

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10.3.3 Reading: Mayo Clinic’s “Monoclonal Antibody Drugs for Cancer Treatment: How They Work”

Link: Mayo Clinic’s “Monoclonal Antibody Drugs for Cancer Treatment: How They Work” (HTML)

Instructions: Please study this page.

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10.3.4 Reading: Indian Journal of Medical Microbiology: Lal, et al.’s “Edible Vaccines: Current Status and Future”

Link: Indian Journal of Medical Microbiology: Lal, et al.’s “Edible Vaccines: Current Status and Future” (HTML)

Instructions: Please study the content of this page. The authors work at the University College of Medical Sciences, Guru Teg Bahadur Hospital, New Delhi. This is a peer-reviewed publication.

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10.3.5 Reading: John W. Kimball’s Biology Pages: “Cancer Immunotherapy”

Link: John W. Kimball’s Biology Pages: “Cancer Immunotherapy” (HTML)

Instructions: Please study the content of this page.

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10.4.1 Reading: Nature Education’s Scitable: Sonia Y. Hunt’s “Controversies in Treatment Approaches: Gene Therapy, IVF, Stem Cells, and Pharmacogenomics”

Link: Nature Education’s Scitable: Sonia Y. Hunt’s “Controversies in Treatment Approaches: Gene Therapy, IVF, Stem Cells, and Pharmacogenomics” (HTML)

Instructions: Please study the “Gene Therapy” and “Stem Cell Therapy” sections on this page. Totipotency means the ability to differentiate to any type of cell. Other potencies are more limited in what the cells can transform into.

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10.4.2 Reading: National Center for Biotechnology Information’s PubMed: Journal of Experimental and Clinical Assisted Reproduction: Jason Hipp and Anthony Atala’s “Tissue Engineering, Stem Cells, Cloning, and Parthenogenesis: New Paradigms for Therapy”

Link: National Center for Biotechnology Information’s PubMed: Journal of Experimental and Clinical Assisted Reproduction: Jason Hipp and Anthony Atala’s “Tissue Engineering, Stem Cells, Cloning, and Parthenogenesis: New Paradigms for Therapy” (HTML or PDF)

Instructions: Please study the content of this page. You can access the PDF from the top right corner of the page. This is a peer-reviewed publication.

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10.5.1 Reading: National Center for Biotechnology Information’s PubMed: Journal of Royal Society Interface: Christopher E. French's "Synthetic Biology and Biomass Conversion: a Match Made in Heaven?"

Link: National Center for Biotechnology Information’s PubMed: Journal of Royal Society Interface: Christopher E. French's "Synthetic Biology and Biomass Conversion: a Match Made in Heaven?" (HTML)

Instructions: Please study the “1. Introduction”, " 2.3. Commercial Biomass Conversion Processes", and " 2.4. Transfer of Cellulose Degradation Capability to Heterologous Hosts" sections on this page.

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10.5.1 Reading: Society for General Microbiology's Microbiology: Rainer Kalscheuer, et al.’s “Microdiesel: Escherichia coli Engineered for Fuel Production”

Link: Society for General Microbiology's Microbiology: Rainer Kalscheuer, et al.’s “Microdiesel: Escherichia coli Engineered for Fuel Production” (HTML or PDF)

Instructions: Please study the content of “Introduction,” “Fig. 1. Pathway of FAEE Biosynthesis in Recombinant E. coli,” “Fig. 4. Map of Plasmid pMicrodiesel,” and “Discussion” on this page. You can access the PDF from the right-hand side of the page. Authors work in the Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Germany. This is a peer-reviewed publication.

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10.5.2 Reading: Biomass Magazine: Erin Voegele’s “ORNL Team Converts Cellulose into Isobutanol”

Link: Biomass Magazine: Erin Voegele’s “ORNL Team Converts Cellulose into Isobutanol” (HTML)

Instructions: Please study this page.

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10.5.3 Reading: Stanford University: Dawn Levy’s “Genetic Engineering Speeds Development of New Antibiotics”

Link: Stanford University: Dawn Levy’s “Genetic Engineering Speeds Development of New Antibiotics” (HTML)

Instructions: Please read this page.

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10.5.4 Reading: Nature Education’s Scitable: Leslie A. Pray’s “Sports, Gene Doping, and WADA”

Link: Nature Education’s Scitable: Leslie A. Pray’s “Sports, Gene Doping, and WADA” (HTML)

Instructions: Please study the content of this page.

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10.6 Reading: Wikipedia’s “Mycoplasma Laboratorium”

Link: Wikipedia’s “Mycoplasma Laboratorium” (PDF)

Instructions: Please study the content of this page.

Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0 (HTML). You can find the original Wikipedia version of this article here (HTML).

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